Hi all, I'm attempting to load an enzo dataset in a directory I don't have write permissions for. I am getting an error I believe because it's trying to write the binary hierarchy, but it can't. I am running Python in a directory I can write to, so can I either have yt write in the CWD or just skip the binary hierarchy? Thanks!
pf = load("/lustre/scratch/darkness/X2560/Dumps/RD0020/RD0020") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/convenience.py", line 77, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py", line 59, in __new__ _pf_store.check_pf(obj) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 152, in check_pf self.insert_pf(pf) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 166, in insert_pf self.flush_db() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 182, in flush_db self._write_out() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 196, in _write_out f.close() IOError: [Errno 122] Disk quota exceeded
sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
Hi Stephen,
ParameterFileStorage is trying to write to your ~/.yt directory. I
believe the error message may be accurate. Try removing the existing
parameter_files.csv from that directory and trying again?
-Matt
On Tue, Mar 16, 2010 at 10:04 AM, Stephen Skory
Hi all,
I'm attempting to load an enzo dataset in a directory I don't have write permissions for. I am getting an error I believe because it's trying to write the binary hierarchy, but it can't. I am running Python in a directory I can write to, so can I either have yt write in the CWD or just skip the binary hierarchy?
Thanks!
pf = load("/lustre/scratch/darkness/X2560/Dumps/RD0020/RD0020") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/convenience.py", line 77, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py", line 59, in __new__ _pf_store.check_pf(obj) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 152, in check_pf self.insert_pf(pf) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 166, in insert_pf self.flush_db() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 182, in flush_db self._write_out() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 196, in _write_out f.close() IOError: [Errno 122] Disk quota exceeded _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
directory. I believe the error message may be accurate. Try removing the existing
Matt, ParameterFileStorage is trying to write to your ~/.yt parameter_files.csv from that directory and trying
again?
Yup. I needed to make some space in my home partition. Thanks! _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
pf = load("/lustre/scratch/darkness/X2560/Dumps/RD0020/RD0020") pf.h Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py", line 150, in _get_hierarchy self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 374, in __init__ AMRHierarchy.__init__(self, pf, data_style) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 42, in __init__ self._initialize_data_storage() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 156, in _initialize_data_storage self.__create_data_file(fn) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 162, in __create_data_file f = h5py.File(fn, 'a') File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/highlevel.py", line 636, in __init__ self.fid = h5f.create(name, h5f.ACC_EXCL, fapl=plist) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/_sync.py", line 88, in wrap return func(*args, **kwds) File "h5f.pyx", line 96, in h5py.h5f.create (h5py/h5f.c:1354)
Just after I sent my last email, I got this. I should have tried this first. Now *this* looks like it's trying to write something where I don't have permissions. Is there a work-around? I don't want to copy the data to a place I can write, it's 2TB. h5py._stub.IOError: Permission denied (Internal error (too specific to document in detail): System error message) _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
Just after I sent my last email, I got this. I should have tried this first. Now *this* looks like it's trying to write something where I don't have permissions. Is there a work-around? I don't want to copy the data to a place I can write, it's 2TB.
What about creating a symbolic link to the data in a directory where you have writing permission? Cheers, Michele
Hi Stephen,
Yup, you should be able to supply:
storage_filename = ...
to the load command. I believe that option is in both trunk and hg.
I also do this on Kraken to analyze data from other users. :)
-Matt
On Tue, Mar 16, 2010 at 10:37 AM, Stephen Skory
Just after I sent my last email, I got this. I should have tried this first. Now *this* looks like it's trying to write something where I don't have permissions. Is there a work-around? I don't want to copy the data to a place I can write, it's 2TB.
pf = load("/lustre/scratch/darkness/X2560/Dumps/RD0020/RD0020") pf.h Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py", line 150, in _get_hierarchy self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 374, in __init__ AMRHierarchy.__init__(self, pf, data_style) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 42, in __init__ self._initialize_data_storage() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 156, in _initialize_data_storage self.__create_data_file(fn) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/HierarchyType.py", line 162, in __create_data_file f = h5py.File(fn, 'a') File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/highlevel.py", line 636, in __init__ self.fid = h5f.create(name, h5f.ACC_EXCL, fapl=plist) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/_sync.py", line 88, in wrap return func(*args, **kwds) File "h5f.pyx", line 96, in h5py.h5f.create (h5py/h5f.c:1354) h5py._stub.IOError: Permission denied (Internal error (too specific to document in detail): System error message) _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (3)
-
Matthew Turk
-
Michele Trenti
-
Stephen Skory